Add specific prettier-commit config for prettier check, improve log message

[mashehu]

Probably preferred to #2099.

Not sure that is the best way to handle the stdout from pre-commit, which is a bit confusing when you don't know that we run pre-commit. It just removes:

  prettier.................................................................Failed
 - hook id: prettier
 - files were modified by this hook

[mirpedrol]

LGTM

When I test it, pre-commit always modifies modules.json, I am wondering if we have different configuration files for prettier, one that wants

"installed_by": [
    "modules"
] 

and one that wants "installed_by": ["modules"] 🤔

[mirpedrol]

I am wondering if we have different configuration files for prettier

Answering to myself, it's the module.json dumper who prints the wrong format every time 😓 so nothing to do with prettier.

[codecov]

Codecov Report

Merging #2100 (a80adbb) into dev (f0b6c48) will decrease coverage by 0.04%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##              dev    #2100      +/-   ##
==========================================
- Coverage   68.01%   67.97%   -0.05%     
==========================================
  Files          43       43              
  Lines        5625     5630       +5     
==========================================
+ Hits         3826     3827       +1     
- Misses       1799     1803       +4     

Impacted Files	Coverage Δ
nf_core/lint_utils.py	78.72% <50.00%> (-7.00%)	⬇️

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[ewels]

Nice! Agreed, much preferable to #2099

[mashehu]

I am wondering if we have different configuration files for prettier

Answering to myself, it's the module.json dumper who prints the wrong format every time 😓 so nothing to do with prettier.

This should have been fixed by #2074, no?

[mirpedrol]

This should have been fixed by #2074, no?

Yes it is :) prettier is run on this file to fix it, this is why I was getting the message The following files were modified by prettier... every time.

[mashehu]

oh, yes, that makes sense! Will be solved by having it as log.debug now.

[ewels]

I wasn't able to break it 👍🏻

[ewels]

(and I tried really quite hard)